In the beginning, it was a giant institution for orphaned children. But eventually it was unsettled and therefore the institution became a lawless district where the outcasts of Fish-Man Island gathered. Fisher Tiger eventually declared himself the boss of the location, and protected his fellow fish-men within the area. The zone consisted of a massive ark where fish-men lived in and around. This was the base of the New Fish-Man Pirates. The Fish-Man District was not part of Fish-Man Island but was located somewhere outside it since Vander Decken IX said he sent the ship on a course to Fish-Man Island while they where already in the Fish-Man District.
The giant ship seen in the district, Noah, is hundreds of years old and awaits the promised day when it will be used for the purpose it was build for. The ship left the district when Decken returned to it and locked it onto Shirahoshi.
After the battle for Fish-Man Island had ended, Neptune realized how long they overlooked the criminals that lived in the Fish-Man District. The king then orders the Fish-Man District to be closed off.